PILER-CR: Fast and accurate identification of CRISPR repeats

BackgroundSequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output.ResultsWe present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes.ConclusionPILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at http://www.drive5.com/pilercr.

• Publication year

  2007

• Venue

  BMC Bioinformatics

• Publication date

  2007-01-20

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-8-18PMID 17239253PMCID 1790904
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Faculty Opinions recommendation of A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.

  2006cited by this paper
• Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length

  2006cited by this paper
• The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes

  2006cited by this paper
• Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences

  2006cited by this paper
• CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies.

  2005cited by this paper
• PILER: identification and classification of genomic repeats

  2005cited by this paper
• Efficient q-Gram Filters for Finding All ∊-Matches over a Given Length

  2005cited by this paper
• CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies.

  2005cited by this paper
• A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes

  2005cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• MUSCLE: a multiple sequence alignment method with reduced time and space complexity

  2004cited by this paper
• Identification of genes that are associated with DNA repeats in prokaryotes

  2002cited by this paper
• Identification of a Novel Family of Sequence Repeats among Prokaryotes

  2002cited by this paper
• Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria

  2000cited by this paper
• REPuter: fast computation of maximal repeats in complete genomes

  1999cited by this paper
• Searching for patterns in genomic data.

  1997cited by this paper
• Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

  1996cited by this paper

• Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.

  2026cites this paper
• Development of molecular biomarkers for monitoring of arable crops colonization with Methylobacterium symbioticum SB0023/3, a methylotrophic bacterium commonly used as a biostimulant in agriculture

  2026cites this paper
• Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism

  2026cites this paper
• Unveiling the hidden viral biodiversity and potential ecological functions with global coral holobiont virome database.

  2026cites this paper
• Biological Foundation Models Enable CRISPR Array Detection Without Metagenomic Assembly

  2026cites this paper
• Seven genome sequences of bacterial environmental isolates from the western coast of the Greenland Ice Sheet

  2026cites this paper
• A prevalent huge phage clade in human and animal gut microbiomes

  2025cites this paper
• Bringing the uncultivated microbial majority of freshwater ecosystems into culture

  2025cites this paper
• The Air Plasmidome: A Discreet Route for Pathogens and the Transmission of Antibiotic Resistance Genes?

  2025cites this paper
• Comparative genomics of Lentilactobacillus buchneri reveals strain-level hyperdiversity and broad-spectrum CRISPR immunity against human and livestock gut phages

  2025cites this paper
• Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella.

  2025cites this paper
• Genome-resolved metagenomics reveal soil and viral drivers of keystone bacterial traits shaping nutrient cycling and soybean yield across agroecosystems

  2025cites this paper
• A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

  2025cites this paper
• Visual Screening of Toxigenic Alternaria Fungi in Citrus Using CRISPR/Cas12a and Quantum Dot

  2025cites this paper
• Genomic functional analysis of the first highly effective Bacillus thuringiensis strain targeting hemipteran pests reveals its plant growth‐promoting potential

  2025cites this paper
• Cannabidiol reshapes the gut microbiome to promote endurance exercise in mice

  2025cites this paper
• Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection

  2025cites this paper
• Advancing CRISPR with deep learning: A comprehensive review of models and databases

  2025cites this paper
• The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution

  2025cites this paper
• Dellaglioa kimchii sp. nov., a novel lactic acid bacterium isolated from kimchi

  2025influential citation
• Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation

  2025cites this paper
• Unlocking the potential of CRISPR tools and databases for precision genome editing

  2025influential citation
• Safety evaluation of Lactiplantibacillus plantarum N13: genomic, phenotypic, and toxicological assessment for probiotic applications.

  2025cites this paper
• CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation

  2025cites this paper
• A prevalent huge phage clade in human and animal gut microbiomes

  2025cites this paper
• Cas12Fold Accurately Predicts Cas12 Nuclease Structures to Enable Structure‐based Genome‐editing Engineering

  2025cites this paper
• Exploring and Utilizing Soil Microbiota: From Dark to Light

  2025cites this paper
• PcoCas12a: A novel CRISPR enzyme from Prevotella copri enhancing TCR-T-cell tumor suppression.

  2025cites this paper
• Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems

  2025influential citation
• Antimicrobial resistance and biofilm formation in rarely reported Salmonella enterica serovars from patients presenting with gastroenteritis in Nairobi, Kenya

  2025cites this paper
• Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type

  2025influential citation
• Casδ, an evolutionary transitional CRISPR system enables efficient genome editing across animals and plants

  2025cites this paper
• Fourteen genome sequences from bacterial, environmental isolates from the Cotton Glacier stream, Antarctica

  2025cites this paper
• Uncovering Cas9 PAM diversity through metagenomic mining and machine learning

  2025cites this paper
• Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations

  2025cites this paper
• Eight genome sequences of bacterial, environmental isolates from Canada Glacier, Antarctica

  2024cites this paper
• Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum

  2024cites this paper
• Whole genome sequence and comparative genomic analysis of novel Rickettsia koreansis strain CNH17-7 isolated from human

  2024influential citation
• Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing.

  2024cites this paper
• Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity

  2024cites this paper
• Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant.

  2024cites this paper
• Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10

  2024cites this paper
• Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum

  2024cites this paper
• Plant growth-promoting rhizobacterium Bacillus megaterium modulates the expression of antioxidant-related and drought-responsive genes to protect rice (Oryza sativa L.) from drought

  2024cites this paper
• Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier

  2024influential citation
• Salmonella Typhi Haplotype 58 (H58) Biofilm Formation and Genetic Variation in Typhoid Fever Patients with Gallstones in an Endemic Setting in Kenya

  2024cites this paper
• Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing

  2024cites this paper
• Viroid-like colonists of human microbiomes.

  2024cites this paper
• Genome-wide analysis of quorum sensing regulon in marine fish pathogen Vibrio scophthalmi

  2024cites this paper
• Salmonella Typhi Haplotype 58 biofilm formation and genetic variation in isolates from typhoid fever patients with gallstones in an endemic setting in Kenya

  2024cites this paper
• The Computational Tools to Identify DNA Repeats and Motifs: A Systematic Review.

  2024cites this paper
• Biodiversity of mudflat intertidal viromes along the Chinese coasts

  2024cites this paper
• Seven genome sequences of airborne, bacterial isolates from Antarctica

  2024cites this paper
• WITHDRAWN: A Survey of CRISPR Across Pectobacterium atrosepticum

  2024cites this paper
• Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions

  2024cites this paper
• Viroid-like colonists of human microbiomes

  2024cites this paper
• Heat-Killed Lactobacillus paracasei SMB092 Reduces Halitosis by Stimulating the Expression of β-Defensins in Oral Keratinocytes

  2024influential citation
• Novel ribotype/sequence type associations and diverse CRISPR-Cas systems in environmental Clostridioides difficile strains from northern Iraq

  2023influential citation
• A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo

  2023cites this paper
• Isolation and Identification of Endophytic Bacteria Bacillus sp. ME9 That Exhibits Biocontrol Activity against Xanthomonas phaseoli pv. manihotis

  2023cites this paper
• Seven genome sequences of bacterial, environmental isolates from Pony Lake, Antarctica

  2023cites this paper
• Infant gut DNA bacteriophage strain persistence during the first 3 years of life.

  2023cites this paper
• Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

  2023cites this paper
• Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12

  2023cites this paper
• Type II CRISPR–Cas System Nucleases: A Pipeline for Prediction and In Vitro Characterization

  2023cites this paper
• Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.

  2023cites this paper
• Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering

  2023cites this paper
• DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery

  2023cites this paper
• Corneal gene therapy: Structural and mechanistic understanding.

  2023cites this paper
• CRISPR genotyping methods: Tracing the evolution from spoligotyping to machine learning.

  2023cites this paper
• Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

  2023cites this paper
• Next-Generation Gene Editing - Current Opinion in Biomedical Engineering Mining Microbial Organisms to Discover and Characterize Novel CRISPR-Cas Systems

  2023cites this paper
• CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

  2023cites this paper
• Infant gut bacteriophage strain persistence during the first three years of life

  2023cites this paper
• Global diversity and biogeography of DNA viral communities in activated sludge systems

  2023cites this paper
• CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing

  2023cites this paper
• Diversity and potential function of pig gut DNA viruses

  2023influential citation
• iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

  2023cites this paper
• Genomic Analysis and In Vitro Investigation of the Hop Resistance Phenotype of Two Novel Loigolactobacillus backii Strains, Isolated from Spoiled Beer

  2023cites this paper
• Comparison of phage and plasmid populations present in the gut microbiota of Parkinson’s disease patients

  2023cites this paper
• ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

  2023cites this paper
• Challenges in prokaryote pangenomics

  2023cites this paper
• Genomic Scanning and Extracellular Proteomic Analysis of Dickeya dadantii DCE-01 Reveal Its Excellent Performance on Ramie Degumming

  2023cites this paper
• Isolation and Molecular Characterization of Two Novel Lytic Bacteriophages for the Biocontrol of Escherichia coli in Uterine Infections: In Vitro and Ex Vivo Preliminary Studies in Veterinary Medicine

  2022cites this paper
• Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20

  2022cites this paper
• Genome editing and bioinformatics

  2022cites this paper
• IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

  2022cites this paper
• Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

  2022cites this paper
• Comprehensive genome sequence analysis of the devastating tobacco bacterial phytopathogen Ralstonia solanacearum strain FJ1003

  2022cites this paper
• Reconstruction of Archaeal Genomes from Short-Read Metagenomes.

  2022cites this paper
• A new family of CRISPR‐type V nucleases with C‐rich PAM recognition

  2022cites this paper
• Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

  2022cites this paper
• iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes

  2022cites this paper
• Multi-color RNA imaging with CRISPR-Cas13b systems in living cells

  2022cites this paper
• CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes

  2022cites this paper
• Metagenomic assembled plasmids of the human microbiome vary across disease cohorts

  2022cites this paper
• Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential

  2022influential citation
• Viral biogeography of the mammalian gut and parenchymal organs

  2022cites this paper
• High Frequency of Dynamic Rearrangements In Crispr loci

  2022influential citation
• Computational Tools for the Analysis of Uncultivated Phage Genomes

  2022cites this paper